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authorJustin Lecher <jlec@gentoo.org>2015-04-20 20:25:59 +0000
committerJustin Lecher <jlec@gentoo.org>2015-04-20 20:25:59 +0000
commit598b41969d936b81faff7e90def2426e973e35c6 (patch)
treedb8e8d8272ad35da39d5b9baafb5961b3309ed7b /sci-biology
parentDrop old (diff)
downloadhistorical-598b41969d936b81faff7e90def2426e973e35c6.tar.gz
historical-598b41969d936b81faff7e90def2426e973e35c6.tar.bz2
historical-598b41969d936b81faff7e90def2426e973e35c6.zip
Drop old
Package-Manager: portage-2.2.18/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB!
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/bwa/ChangeLog6
-rw-r--r--sci-biology/bwa/Manifest38
-rw-r--r--sci-biology/bwa/bwa-0.5.0.ebuild29
-rw-r--r--sci-biology/bwa/bwa-0.6.2.ebuild35
-rw-r--r--sci-biology/clustalx/ChangeLog5
-rw-r--r--sci-biology/clustalx/Manifest35
-rw-r--r--sci-biology/clustalx/clustalx-2.1.ebuild39
-rw-r--r--sci-biology/dialign-tx/ChangeLog6
-rw-r--r--sci-biology/dialign-tx/Manifest37
-rw-r--r--sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild8
-rw-r--r--sci-biology/dialign-tx/dialign-tx-1.0.2.ebuild42
-rw-r--r--sci-biology/finchtv/ChangeLog5
-rw-r--r--sci-biology/finchtv/Manifest35
-rw-r--r--sci-biology/finchtv/finchtv-1.3.1-r1.ebuild32
-rw-r--r--sci-biology/paml/ChangeLog5
-rw-r--r--sci-biology/paml/Manifest35
-rw-r--r--sci-biology/paml/paml-4.4c.ebuild43
-rw-r--r--sci-biology/wise/ChangeLog5
-rw-r--r--sci-biology/wise/Manifest36
-rw-r--r--sci-biology/wise/wise-2.2.0.ebuild69
20 files changed, 139 insertions, 406 deletions
diff --git a/sci-biology/bwa/ChangeLog b/sci-biology/bwa/ChangeLog
index c491255338d6..17f8a4893c1d 100644
--- a/sci-biology/bwa/ChangeLog
+++ b/sci-biology/bwa/ChangeLog
@@ -1,6 +1,10 @@
# ChangeLog for sci-biology/bwa
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.18 2015/04/19 09:59:46 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.19 2015/04/20 20:21:41 jlec Exp $
+
+ 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -bwa-0.5.0.ebuild,
+ -bwa-0.6.2.ebuild:
+ Drop old
19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> bwa-0.7.12.ebuild:
Stable for x86, wrt bug #544944
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index d14fc0f9fc9b..6174cc4fd37b 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,29 +1,27 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
AUX bwa-0.7.12-Makefile.patch 911 SHA256 b67d36d5fe755f572cf8b5998e5dedc0545e89aa6eb7ca808327f06f592c132a SHA512 17fb2f1ff580c0f6cbe54501fa968cf554c9fb07b5b1190e61f786317c27f769a2475867a5f935ee82055007fc16e14589efa852e674ee49d423bc3283572b37 WHIRLPOOL 54d8b0273b2a20eea7835802ede06f04209b2b3f95fadfb7435d3a7914ee8df6c4fe0c7f911bdcc5d1be533ca80c5aac718f3320dac182f27f1d8d0eea6d87fd
-DIST bwa-0.5.0.tar.bz2 103638 SHA256 02749e290d07ee7c96a9d219be7290f4b0f21fa6fc8e1405d8a6a657cd0dbc77 SHA512 5378072bfc54a3143de71ea34f821e745707564183b790366310a83395c07f37bb836cff3dc1743a5db97065595baa2bd5243f74abf07ad09878344ab85bce08 WHIRLPOOL 9a3ab47d7e7532a21e2d3a3a9d6e29aab551392ca87bb13360e768f06169380ebc32dfba88ffc3e822ea057752b61a56c76042ca3a63257473f51d8fb996349f
-DIST bwa-0.6.2.tar.bz2 128409 SHA256 8783e5640d8e4ae028e048c56db1d6b4adff6234d1047bd4f98247ffc3be69e6 SHA512 c0fa98c488839062e681f2879f7edc882bfaa99e978c4c075eaa967fcfc2d3eb626c66fd8a998794d4c5e72559594d3dde9b5cccc5baf5e1fbff167c73a5a63b WHIRLPOOL 448be4cb092d45c6649069b5ac36feb29c7671e9bc6d8c9cc51394a0c97f89a21a9ef8564774d9de1e6c7a66b900d93cd4cac55ba890b6889fb2d59c0a51033e
DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0
-EBUILD bwa-0.5.0.ebuild 665 SHA256 fe6a5dd9d7439ef97a1cbe94d0facb29dbc513e5c6fdc7944151850307205f3f SHA512 48c07646e27a787c9acb248866fae68def77cd2c9cde363d27013593cfedb4b5d5418497e3ce771daf999d0d3d548ecc5d66cc7d36996a2540b37027e67dc4c8 WHIRLPOOL 2c283bf4d8e40dacfac95c1470cad311cc5ede18963004ba3897f0cef0a9ca7750d4f08480f3dfe3d563dfae1ad869b3f98a525597d916bf43f36585c37add97
-EBUILD bwa-0.6.2.ebuild 870 SHA256 16b8d1bc0542261324e189f0331ac7ece261bc66c988affe177d6c49cba27280 SHA512 6b6f1b39fd795745e48cf72dfb67a6860002d117f9cc3615bd8cea261d95b850120322913028e914dc35b90698828d81cdc214c77e1a67b5634bfc8c674add77 WHIRLPOOL bd960bf958ab3a40c6c648f7cdbef849028f0624cc766cf110334fedcf8e243e16f32ee341cad02f995258b6b9f7216af368d3d7b823cf2ecb84de7f940c984e
EBUILD bwa-0.7.12.ebuild 748 SHA256 04f6e20b53787c373c637b3d47a7f7166c41b6db9cf3931ebcc793f3868037ae SHA512 17db5bbf3eaf7a0a8ee0d2b635cadaa5a77c8476edb8c16a6fc37b99e8ac3c0c0553a8c887191d3a7f66aa54de1e281ce981125ae0f77a56357b85730141ffb1 WHIRLPOOL dd778d1b05199f59657dfe71b0a9c4313c4160b73ea2bd68e683dcf0a910f251a9663033173941ae7010b9794cba2e0b53f12c48b64b59710f4b3b0869461b6e
-MISC ChangeLog 2497 SHA256 064f571a286d78e0039a7c3bb8d6fccf6611c8df6245cf44f73ded541b39dfd5 SHA512 c8f1ba13f558156574c58d5c84d92f1798b92a30deb775dfe2e06e213be8a53db02481762e966375fbb1e4a90c8d07c6caab322c43ca6e8831fd677749747246 WHIRLPOOL bf122a698f78dfa88879ad2f2091d19f29cf0f1d0e054ecbd4df0ee3e125668f4ff81849ed35c6a7d289687a7d01971784cc1b0c38114063189014c053d9db46
+MISC ChangeLog 2597 SHA256 ea33c05fa080e2b98f2ceff38591e4a057b2214cdd58c04ba19daebe51d45343 SHA512 526bf2b02393e7b652fda2b64f5af2c2510da6ac4d88f846de4df6180e52f2894d3b4e940dda020caaa506ce5b6ee7f477117c8ab9348801b043ff21f4d078ef WHIRLPOOL 5076ca1b5a01dae4c891c652fff9ce91ab3ca4aea2a1df7a46853e4e9e0a48829ba38e745cc9aa3fe5b72ab96ef5623cc03bcc490e9b5cb1b3e8271140e05a6c
MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/bwa/bwa-0.5.0.ebuild b/sci-biology/bwa/bwa-0.5.0.ebuild
deleted file mode 100644
index 0a8f3b2177cc..000000000000
--- a/sci-biology/bwa/bwa-0.5.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.5.0.ebuild,v 1.3 2010/05/23 21:15:12 pacho Exp $
-
-EAPI=2
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="http://maq.sourceforge.net/"
-SRC_URI="mirror://sourceforge/maq/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND=""
-
-src_prepare() {
- sed -e "/^CFLAGS.*/d" -i "${S}"/Makefile
-}
-
-src_install() {
- dobin bwa || die
- doman bwa.1 || die
- exeinto /usr/share/${PN}
- doexe solid2fastq.pl || die
- dodoc ChangeLog NEWS
-}
diff --git a/sci-biology/bwa/bwa-0.6.2.ebuild b/sci-biology/bwa/bwa-0.6.2.ebuild
deleted file mode 100644
index 9430a23b2e0d..000000000000
--- a/sci-biology/bwa/bwa-0.6.2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.6.2.ebuild,v 1.1 2013/01/21 06:15:22 weaver Exp $
-
-EAPI=2
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="http://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-src_prepare() {
- sed -e "s/\$(CC) \$(CFLAGS)/\$(CC) \$(LDFLAGS) \$(CFLAGS)/" \
- -i "${S}"/Makefile || die #336348
- append-flags -pthread
-}
-
-src_compile() {
- emake -e CC="$(tc-getCC)" || die
-}
-
-src_install() {
- dobin bwa || die
- doman bwa.1 || die
- exeinto /usr/share/${PN}
- doexe solid2fastq.pl || die
- doexe qualfa2fq.pl || die
- dodoc ChangeLog NEWS || die
-}
diff --git a/sci-biology/clustalx/ChangeLog b/sci-biology/clustalx/ChangeLog
index df4de608e9a6..7d4baba9d2fa 100644
--- a/sci-biology/clustalx/ChangeLog
+++ b/sci-biology/clustalx/ChangeLog
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/clustalx
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/ChangeLog,v 1.32 2015/04/19 10:00:03 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/ChangeLog,v 1.33 2015/04/20 20:22:12 jlec Exp $
+
+ 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -clustalx-2.1.ebuild:
+ Drop old
19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> clustalx-2.1-r1.ebuild:
Stable for x86, wrt bug #544936
diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
index e3141444e28a..8d43686de463 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,25 +1,26 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
DIST clustalx-2.1.tar.gz 341649 SHA256 e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 WHIRLPOOL 6cbe8dcf2be3a535e8ac0ef0b9b476d4429a80bd94b394c0194f46ed039f9ac2b97b0ec2ed680838a0973b3187b2dbc90285733657975e03288b9840ba3d6b15
EBUILD clustalx-2.1-r1.ebuild 1208 SHA256 e5323a8d536f1000bcc218f747a5c812f45cbd1dfef6a276131bc247be0f175c SHA512 ca497dab1bb4cf43d9ae19df0c005fe1cb96a0ed8c267d73a104559652956b89a17acf3931e5f667445f2e40ba628f965d1954d6696a093ffc7d66c095e7cb61 WHIRLPOOL 2fd7c3276ffd58f974de4bd7fc8643db5d3536aeea002ee952261514d23e2ca6a7048c063816e415776c78cc33c2511957769b6a3054d17b710a6d8ee0ccce97
-EBUILD clustalx-2.1.ebuild 1145 SHA256 ce7958e660ea79a47cd4956972eca3993eb45f6824fc29813d04d7b524f88a6b SHA512 6e754244290dbbdc04ff76c50704ece6a28c3add64d6efa6d178a2646af4ae75d903e9a710a80d40e10aa8141c53705d3b2ccbfdc3230585843bc6ee17a99af9 WHIRLPOOL ea8e4acafa4d948671eebaaccfff9d6da37bc280ee7797bd9a15ba90f1846c2b4094b410d220f9d2ead90b86e8fc2608eafb3d450a74689be7c34451918e1031
-MISC ChangeLog 5203 SHA256 20765293e7b76c20d973483fc083a7fd6ecb51140465cb2f7dcd5e25d4395494 SHA512 82e31f249b17d9d2e065a9469181eb7845c4eba1bcfa9c151094304d6e19293e3ecd93713ac60fefb6bbcc8e1b37e624bb16b5ccbaab106d4b2d9f79e8ca4791 WHIRLPOOL ecd9d9b1c233dfe82f4a20d49fe25bcb9fdad489b6d6ae31e34d193dc159dc5e2f749a4b11bfd41dbc2b3f89e0196fc1aad1448433326a718a829f8fe651425a
+MISC ChangeLog 5285 SHA256 488232e993e1a5d379fd4335175226efa20b7a19d120c84aa2b23406409abf15 SHA512 07c2a77c647da4bedf95a9f353de9353f90f51b838379a0eef96d401ecd073688283991a200cf1d0b93e726db3d38dd60c1def58b1ba132a1ccf65efad328e7f WHIRLPOOL 984359f1319c3a55cf2cf722c026e65405d749287b5367b9379a82502bcf0ce0911ade41d6e2fab8ecae30b77d81d7bb5be2d43079033c964f395dd26e9fe8fc
MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+RsYM7c7pqODShPx7m6di
+=NEq0
-----END PGP SIGNATURE-----
diff --git a/sci-biology/clustalx/clustalx-2.1.ebuild b/sci-biology/clustalx/clustalx-2.1.ebuild
deleted file mode 100644
index 858984b48a8c..000000000000
--- a/sci-biology/clustalx/clustalx-2.1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/clustalx-2.1.ebuild,v 1.4 2013/03/02 23:15:41 hwoarang Exp $
-
-EAPI=4
-
-inherit eutils qt4-r2
-
-DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
-HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/"
-SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-DEPEND="dev-qt/qtcore:4
- dev-qt/qtgui:4"
-RDEPEND="${DEPEND}
- >=sci-biology/clustalw-2.1"
-
-src_prepare() {
- sed -e "s|colprot.xml|/usr/share/${PN}/colprot.xml|" \
- -e "s|coldna.xml|/usr/share/${PN}/coldna.xml|" \
- -e "s|colprint.xml|/usr/share/${PN}/colprint.xml|" \
- -i ClustalQtParams.h || \
- die "Failed to patch shared files location."
- sed -e "s|clustalx.hlp|/usr/share/${PN}/clustalx.hlp|" \
- -i HelpDisplayWidget.cpp || \
- die "Failed to patch help file location."
-}
-
-src_install() {
- dobin clustalx
- insinto /usr/share/${PN}
- doins colprot.xml coldna.xml colprint.xml clustalx.hlp
- make_desktop_entry ${PN} ClustalX
-}
diff --git a/sci-biology/dialign-tx/ChangeLog b/sci-biology/dialign-tx/ChangeLog
index e11072e52395..c61581ec2dfe 100644
--- a/sci-biology/dialign-tx/ChangeLog
+++ b/sci-biology/dialign-tx/ChangeLog
@@ -1,6 +1,10 @@
# ChangeLog for sci-biology/dialign-tx
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/ChangeLog,v 1.7 2015/04/19 10:00:20 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/ChangeLog,v 1.8 2015/04/20 20:24:44 jlec Exp $
+
+ 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -dialign-tx-1.0.2.ebuild,
+ dialign-tx-1.0.2-r1.ebuild:
+ Drop old
19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> dialign-tx-1.0.2-r1.ebuild:
Stable for x86, wrt bug #544948
diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
index f561ea04ae32..847322458c73 100644
--- a/sci-biology/dialign-tx/Manifest
+++ b/sci-biology/dialign-tx/Manifest
@@ -1,26 +1,27 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
AUX dialign-tx-1.0.2-implicits.patch 776 SHA256 c13bfae6c2ffa4a676fc92a1dbe7f82d08578e5f36add057d0ad84a955aa7ca5 SHA512 632da19c24834f011778e1be23a8b19f64da4e52386c99838393f678e927174bd8d3d9d175716e2651fcb884673123136166c401d3e687b882e5eaf69d597a1b WHIRLPOOL d5fd29ad957ffc734d4ef24811e3f131f86bfa2ffd4bd41da4353fd10f1a3a370e6ac531a943ded7fe908b89373e32e857d478e80453889e41aa1d102db272ea
DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277
-EBUILD dialign-tx-1.0.2-r1.ebuild 1117 SHA256 0f485642e3973eaec7a3ea14311fac2cb4513275ea184966aea701e2e7c273ad SHA512 40e47e21b3425b42c296c1689a324d9c3a7def8cdc37b0b04007aa82b92d252f3170c03c971ca05d46ec2f1f70f01209590a2c675bf358543768d1c46b929ce5 WHIRLPOOL fcb840c448994c7fe6044f14b06c44c4cc1fd07097c25bbb172949e0b6bc2d760d350934e42469a0cfa8f47c18ab3726db77c7f8ee910d5371ca52d06b2875db
-EBUILD dialign-tx-1.0.2.ebuild 988 SHA256 c9988b388b6acfbd18302b95d6597822a6b4dd762bdee9b5521e9de0043d0d39 SHA512 3628782bf11323aa5353a8723ad26819aa35f6835a9e168ebb4f617f915171ea98c77faf44e9a16648bf1f71a3ad4e510622ccb061a098032b125e3740e10a10 WHIRLPOOL 008c2ef3fbd5beb144dbf9ddbac196606dccd80f86a6d4e690c17f672382106df3dfec42b38c539c9d4da3329aa5949bc3155f8273714ae3557463c23eeca721
-MISC ChangeLog 2339 SHA256 18159b4e9192954ea5c5f63735c8e9197854ed7a7c58e7419baf77a7a27eb159 SHA512 0dc670b32c28c15b3960663a686ff5ff5ed32f4e29b3677bcb74f3ea139bebc1c60cc387a15f8e852e9b5dc40d405ac13d47815f44ad46e52289e58a4f89575d WHIRLPOOL 54a13c133134b2ad28afdbb5ad91a5391f8fa286fdd25773db6fec137ec876809c7f4bc07dc0232d55d28d5c947350830cb8ced679687c13e18d67912e15c2a9
+EBUILD dialign-tx-1.0.2-r1.ebuild 1081 SHA256 eaddce092520584bff8852ff38b45e42c2a19d0aecd9c1879c53439b0c200913 SHA512 62493a58f405f06317ea3cb9d88f157818b06ec2a9f00cba248d873649dcdcfc03090e80a1e056358e0f134ae50a13879275cb7569059c9668876de18f1536ec WHIRLPOOL 500c585bee283d59232dad8da2e80083955fd2d86a4c3452375094391d23695208d742643c7dc60b1c5a911344242d6e49d0dc7e3ef64ed4b63f151272769136
+MISC ChangeLog 2455 SHA256 826243159ec72a293d7fdd92561bfa034991227eb8cff363a272dec0211c2986 SHA512 f36fbf5567d04ed9b3880480136a1524a562160d4cd8c6092c4df7a0ef05d3ddde9e483016dbc32f60ca2de5706f9bd2c0a77464c1ffe767d7f4a9e636533dd8 WHIRLPOOL 873a2d1aa9ff64633684ef3195909e92ef0a2d3d6ff4dcb4c1a828c4d0511eea82e93f03c5e660e4116e83135eaca59f369d88c0344831c871319ad8c2f1081f
MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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-Version: GnuPG v2
+Version: GnuPG v2.0
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diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
index 6297b1b4aa91..38a5edbba5ca 100644
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
@@ -1,8 +1,8 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild,v 1.3 2015/04/19 10:00:20 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild,v 1.4 2015/04/20 20:24:44 jlec Exp $
-EAPI=2
+EAPI=5
inherit eutils multilib toolchain-funcs
@@ -28,11 +28,11 @@ src_prepare() {
src_compile() {
emake -C source clean
emake -C source CC="$(tc-getCC)" \
- CPPFLAGS="" || die "make failed"
+ CPPFLAGS=""
}
src_install() {
- DESTTREE="/usr" dobin "${S}"/source/dialign-tx
+ dobin "${S}"/source/dialign-tx
insinto /usr/$(get_libdir)/${PN}/conf
doins "${S}"/conf/*
}
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2.ebuild
deleted file mode 100644
index 04d5198f5809..000000000000
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/dialign-tx-1.0.2.ebuild,v 1.3 2010/02/09 11:20:45 pacho Exp $
-
-EAPI="2"
-
-inherit multilib toolchain-funcs
-
-MY_P="DIALIGN-TX_${PV}"
-
-DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
-HOMEPAGE="http://dialign-tx.gobics.de/"
-SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/${MY_P}"
-
-src_compile() {
- emake -C source clean
- emake -C source \
- CPPFLAGS="${CFLAGS}" \
- || die "make failed"
-}
-
-src_install() {
- DESTTREE="/usr" dobin "${S}"/source/dialign-tx
- insinto /usr/$(get_libdir)/${PN}/conf
- doins "${S}"/conf/*
-}
-
-pkg_postinst() {
- einfo "The configuration directory is"
- einfo "${ROOT}usr/$(get_libdir)/${PN}/conf"
- einfo "You will need to pass this to ${PN} on every run."
-}
diff --git a/sci-biology/finchtv/ChangeLog b/sci-biology/finchtv/ChangeLog
index 70f4bb5f167a..09a4aaccd519 100644
--- a/sci-biology/finchtv/ChangeLog
+++ b/sci-biology/finchtv/ChangeLog
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/finchtv
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/finchtv/ChangeLog,v 1.10 2015/04/19 10:00:57 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/finchtv/ChangeLog,v 1.11 2015/04/20 20:24:42 jlec Exp $
+
+ 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -finchtv-1.3.1-r1.ebuild:
+ Drop old
19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> finchtv-1.3.1-r2.ebuild:
Stable for x86, wrt bug #545798
diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest
index d1f4933fa3ca..5c59ab991265 100644
--- a/sci-biology/finchtv/Manifest
+++ b/sci-biology/finchtv/Manifest
@@ -1,25 +1,26 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
DIST finchtv_1_3_1.tar.gz 6706911 SHA256 03fccbf1ab09b571bbf55d0b71dd86975513b7a6c8d54795055a184b4eda8858 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8 WHIRLPOOL 3b6de1673b69bfb41f1416e7758ccafcf97f10bd4f348a88e8498d04c408caf2ac316d8e1a20bf1abe2d6487f38c3b9875af54ecb1d2b1a2ff813b436de90988
-EBUILD finchtv-1.3.1-r1.ebuild 886 SHA256 b4afa95028546250da4692069ded67d31034ce0a0270f55e8e3eeb57cf1a1452 SHA512 210cd815b0964821f6113d9035147b95ab93e658449f2790ff05ba26ce62c470f4cb97ba2cd40f9bda9879b72caf5ca21a6b3c631183cf8e1c2b34694126016a WHIRLPOOL 411cec8ae35fe6ef46de5e2d4b4f845dccc6388dbd6bf0a31f524c87df14a70a1eec47baa286f8622841e0ac9b435a53b5c9aa4660bccf0e8f0155391fe22ee8
EBUILD finchtv-1.3.1-r2.ebuild 725 SHA256 8148c6f7869ded647dd322cdb61e9b302823818eafd66bb5dddc2ad2fd32276a SHA512 8b3662d27e952465041d4718f0a91583d312be0e336926f7b3175743a549af88dc4d380d54971b71688c90ef841d787283dae3b13d2e6ad09c0a71d67386edfa WHIRLPOOL 35a55be47671d0d896d8890c2329f36c55a82774b8c451bdf27edc8f87b172adc751cf8e5515b0e6920d12d7e16714e2145f4c78a76f462ff99afcdd92870808
-MISC ChangeLog 1457 SHA256 6555d375d6a9ac74c6d778ac7d4d0e7b80c7b57b622b2f671f47aa464b3b080f SHA512 15955c4ab8b4fa572ecdf118d6ed450ecaa34023269c4c86a2462ea8a7535443ba1b863b37d4361f0e3f21945aaf7f595b1d90516ea38b372a6a54b67ab8bf7f WHIRLPOOL 75d7c0c4b7f1ae603b8deb5d69082843d2e8779422fa0675c26b5e3a2972e53ee28d40dfe3d2f6577299b4368bbff92f4c9f31121d99a8fb38b5a3d534d85a31
+MISC ChangeLog 1543 SHA256 bb5e832b6b77f943d4b4870c90e3ed2a28eb0af68cc2f876ea277a3ab7b45b42 SHA512 225709a2660ec56d6fd26f857f08b2530c1f4016c4fe7ffdc30f7b9b7d8071d2a67f8a158b8b57029c59ec035f06d15ffcbec26508d2a04a7b2c80922d2414b2 WHIRLPOOL 6b6d61b912a9dc1abfce7bea0108cbee9fca5f9190f7272beb8212dc9eca1230e7f41466ddda08b552e0a203662032093ab5e054b09905dc9b43bc9ceaf4e8f3
MISC metadata.xml 371 SHA256 3bc424643ef6623429dc11a60c7ee16306c0448ca77973e8da73a4c48d76dcbc SHA512 277b888bf1ea00fd006c88902b84a94f116dc992a466c61c06f47c965517ba103138e32c8fd6fe934f340e38597194b3efaae4b57a3ad500a46375bd06625ffb WHIRLPOOL 4897df64f446e645d5f6c11c5a99824a3ec9dba2d9414c393f9e7aaed059fad391ecf739ee9ad89127b5c4e977beb2e01c391f0e3609f824cb315c358d86c1ee
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diff --git a/sci-biology/finchtv/finchtv-1.3.1-r1.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r1.ebuild
deleted file mode 100644
index 8968ab7db677..000000000000
--- a/sci-biology/finchtv/finchtv-1.3.1-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/finchtv/finchtv-1.3.1-r1.ebuild,v 1.5 2012/07/24 12:22:42 jlec Exp $
-
-MY_PV="${PV//./_}"
-MY_P=${PN}_${MY_PV}
-
-DESCRIPTION="Graphical viewer for chromatogram files"
-HOMEPAGE="http://www.geospiza.com/finchtv/"
-SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz"
-
-LICENSE="finchtv"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}"
-
-QA_PREBUILT="opt/bin/*"
-
-src_install() {
- exeinto /opt/bin
- doexe finchtv || die "Failed to install executable"
- dodoc License.txt ReleaseNotes.txt \
- || die "Failed to install docs"
- dohtml -r Help/* \
- || die "Failed to install html docs"
- insinto /usr/share/doc/${PF}/
- doins -r SampleData \
- || die "Failed to move SampleData"
-
-}
diff --git a/sci-biology/paml/ChangeLog b/sci-biology/paml/ChangeLog
index 7dc0b1c83afe..688564fbd8fd 100644
--- a/sci-biology/paml/ChangeLog
+++ b/sci-biology/paml/ChangeLog
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/paml
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.19 2015/04/19 10:01:48 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.20 2015/04/20 20:25:35 jlec Exp $
+
+ 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -paml-4.4c.ebuild:
+ Drop old
19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> paml-4.4c-r1.ebuild:
Stable for x86, wrt bug #544958
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index ec304ce09c24..67f6092edecd 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,25 +1,26 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
DIST paml4.4c.tar.gz 2891715 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a WHIRLPOOL 44ae42dd6088039be1041cdce70ce9ee907b8f85d4e25f9d556df4738ea3ea91f700f96f627f20a13d226038132fd23aecbc5b452bfb6716b9499c8d2be491e4
EBUILD paml-4.4c-r1.ebuild 1091 SHA256 6d721c128a5e47882f4fa0f6af57b0c5011b9b6980839daf83061fa3b6267859 SHA512 cea489d1dcd133ab2a26c5bf7757a67cae295d6dea8ec64e47b5537d4928f2fe3a0027cb3520faa6091264cee56ab8d51368e45430e9701ebf0db415b6d5c8d5 WHIRLPOOL fa991c94d3622a55e55e707c33b6f3ce5960771d89b34fc78a858ade143cd76565e47d45f617055c19cca159f3f151ef0d16711bb40c1e3d5a1d954456cfe2c7
-EBUILD paml-4.4c.ebuild 1209 SHA256 558abe2195e74b8759b55a46c87e2381fa052956b75fb286925b5fc45516e1be SHA512 2163475154045d40417fe66af89a5be253beeea514ae4fd4a619dcd9cfb09c78d24a4f7c4652b7235d340731b1b8877a2a2a2a46c1210196dd8da15005abd2ba WHIRLPOOL 100802ed26aea0ef176ee4ea7557330e86ca3e62dd579741ef13ed045a479ddcb67bc1cd9521e15be8c4991d3488758338f00f8631039b65c9a66463f9c6992b
-MISC ChangeLog 2551 SHA256 06811f16ed3439d76decc8c81fde46e932e90c5a737d18e32443f0ec478c25b2 SHA512 3fe031c9b7abbcde2b049572cd329d721cbd0f691d40f2c41968d60982c8ecef80942ce1b7b5f2b42c26e29a887cd293b77367116eceba2d41e786ba2cfa4e0f WHIRLPOOL 310673bf6b4a76f72099675ac00e9c736495400a9c446ed1fd501ad64d825bb0d65a8667bf0003ad0fbe40b7f54a55281c3ba4be6bf22fabbf2c38ef5abdb313
+MISC ChangeLog 2630 SHA256 6c2d59aeba797855630a7d38aaae91f36b31d2b2a48e71a7798d89901a3bffe6 SHA512 baed8489c9c2684a208f9f42096a299d268048ea19a0c71e43bc4f17a9f8438f14ab702c31bb4c252bddd6452469fa7641ba6694a7899d22ab9ee2f02df8f8eb WHIRLPOOL 19701038e949a640bedf1caada118ec3272591c45f215c66c0c355fcc5445086f925a7e8e4060064a822ecdec75ad8c4d4765499aaaeda8b25670c9b801febf1
MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
-----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
+Version: GnuPG v2.0
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++Q18JBriVZ3xviTeRmNy
+=qO7i
-----END PGP SIGNATURE-----
diff --git a/sci-biology/paml/paml-4.4c.ebuild b/sci-biology/paml/paml-4.4c.ebuild
deleted file mode 100644
index d9dd2e326f3a..000000000000
--- a/sci-biology/paml/paml-4.4c.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.4c.ebuild,v 1.3 2010/09/12 16:16:35 hwoarang Exp $
-
-EAPI="2"
-
-inherit toolchain-funcs versionator
-
-MY_P=$(version_format_string '${PN}$1$2')
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
- # Notice send by mail to prof. Ziheng Yang
- sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
-}
-
-src_compile() {
- emake -C src CC="$(tc-getCC)" \
- CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" || die
-}
-
-src_install() {
- pushd "${S}"/src
- dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 || die
- popd
- dodoc README.txt doc/* || die
- insinto /usr/share/${PN}/control
- doins *.ctl || die "Failed to install control files"
- insinto /usr/share/${PN}/dat
- doins stewart* *.dat dat/* || die "Failed to install data files"
- insinto /usr/share/${PN}
- doins -r examples/ || die "Failed to install examples"
-}
diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog
index fd0d0edf8f34..088b9929611a 100644
--- a/sci-biology/wise/ChangeLog
+++ b/sci-biology/wise/ChangeLog
@@ -1,6 +1,9 @@
# ChangeLog for sci-biology/wise
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.20 2015/04/19 10:02:55 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.21 2015/04/20 20:25:58 jlec Exp $
+
+ 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -wise-2.2.0.ebuild:
+ Drop old
19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> wise-2.4.0_alpha.ebuild:
Stable for x86, wrt bug #544940
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index 1e07f86a81c6..1d8c8a3d7689 100644
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -1,31 +1,31 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
AUX wise-2.2.0-glibc-2.10.patch 7044 SHA256 92086174f059ab9732cf502acd9619fc5c9e1c34c5018b6c493d5203ec629503 SHA512 9e9ce8a5954b5cceee6bfff8af49d9d085e5bd5b922033bd2bf539d27bcdee6dd531a7fb5a17bf317decc6f870eb95184974cc0b724cf5531a2fb52306ac8357 WHIRLPOOL ed56101ecc68ea776359f1fa578a98ca2b4d60046e4e6d8482be17075eb8ec9d77408e223a2dd4f63773053f24f60787d8a9285f21213441405b6beba57ccfe7
AUX wise-2.4.0_alpha-cflags.patch 27241 SHA256 281c95e7f37f217a9bd730ba4d80640a6085dc134fb3dcd837f217b36f5b5b87 SHA512 2f4faaff8198c63fb22edde934584fa2d00d2a333c5caefbbbc569e6136546aa274060453f093e0791a4d61bc901e1f199c47bb60d1be9f0ac32b3709cb025ab WHIRLPOOL 2b48020dde9e0f19a3ff32f2db6d0d08ea5626e0f11eb8560c23160ae716fa55ac3a2946bcfb6e90c018db98df7ee38eb66f44acef6828d29f67d00fbd9f58d6
AUX wise-2.4.0_alpha-glibc-2.10.patch 8068 SHA256 caaacdde33b1f0b12aa0854fa27e3b2c4d6bab099dbc627e18057609763ce265 SHA512 eba50ed8e12ca94d026fed95602ec1d1683ea26f0195952304a1caebdb94df700b547168a6da4a9ad4289dd9c6060572b4ed9dcfcc7698dff2812765adc556e1 WHIRLPOOL 38228826603523ab1d5d31b02e57016e128788d3767820f6a2efb79234f01e6ffec63480430c5ec7cf21ea24351aece8ad0303ea7ec0aacfa4868989bb4a82dd
AUX wise-api.tex.patch 2234 SHA256 31042f660669ea9df9bc608006cd40479e004f5cbb9aed055d3ec58a853c145d SHA512 1cb7b5f5377d4d235707d32d74087598db5abc793b2aba8272a7da941a25d5618691212240eb25c078df39868ea7adfacfba3d218bd77fcea5d57b3b2ef51a0b WHIRLPOOL 523d0b0fa7c97669ca1e4e2229bb432ebe1002d7d0249064217591b0c542d4fc6171e5e924bd650c71d46e02d4c180b2763d1b1f1d87b077a55cbf1e53e3c6ac
AUX wise-env 40 SHA256 de6f742147c43b3820ea261fd158647ae1d2d9e8fe562e0b5c4c0d7e878ced36 SHA512 58cfa40d4d3b2623df82bb321f8dd2f5ebbee099ccfd4ac0e3eb9edf5693dbaee0581f8986b4923c60060d92c028e731f15c047e18f86efb76adaf4ec386e96c WHIRLPOOL 62228e902a0b962ad13514b76a2fe52eb3d6626c7536d63c3425c1e11abed08f4c9e971b7d30b78950e3ba0fbf5e020cd6286148419692f5c6d93876e0e6a8eb
-DIST wise2.2.0.tar.gz 2108151 SHA256 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780
DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec
-EBUILD wise-2.2.0.ebuild 2057 SHA256 04fde7ed22aa32ece4421616fa532a4616b954d5d822560b82a0160a5f34f10d SHA512 c618a179cf4de50acdb38d32b22ef79c2d3d377c4839d862865da15adfd09028448550a1bab5d9e11e125ed28aa0e809782971d42ca922ed4927e0a7f763b9c4 WHIRLPOOL 6e198616ce821feed1fb790285451ce6073b4c28838d76d3d0a44f60aa8766cf699a2fe15c0fc8405ea02e0990090622e300eb21316632effdb890c11bfb20d7
EBUILD wise-2.4.0_alpha.ebuild 1758 SHA256 4280770382335ccea1d91421cfb2eb48ca37ed6e06272b61d88c1f5b16e28115 SHA512 40faa8cf96d760220b5b21557a20d0b155abb27bac5cff5ddc7de9729f6011a50fcf082e76ffc11e56749c3520e7c03f109417d248511deb043112a53518ce0f WHIRLPOOL d8f53f5c2bb9010b300e025107e9d8378cbc2b5738310368944ad30b5c59ccd2f0ac0e393c4d1026c2dff8f2c1b6d4aad3903fa248fd7dbab00b8ae043402c93
-MISC ChangeLog 2878 SHA256 55abc9538411106edb639f4d427f137b43885a595c71c3435c86478aa7d09b2b SHA512 d7517644943e4866fea50bff7936d13c142be01f9b458a522878db4073e2d227ef3bf1ecde11b66e1098fcdce8d2c4f374816eb26e6c25d0069583ac049be114 WHIRLPOOL e7a6f04a332fcdcf5a84a37308071c5df70a96a69675e633e461f9bd59604ac63285f0ca27d86ea259e07fd5858bc14590a25996faeee77bc2f1faea0c889273
+MISC ChangeLog 2958 SHA256 89da20b9ff628f1582a29544932a00af4f071b41d49c6dcc12fae19465544ac2 SHA512 6342c0e4b676dca1698bae42a470d0f931528791cb6a77b239609c74986b2e80574e6372308d1aef91bb23221d7719a052079bb51b5196c24f90fa89cb75141f WHIRLPOOL 9e22b0b177da5773f6f0be267ea8642c64ac49c0be1167a7896054866ec5d596f879b915229fefd6a934e636629ce7a145b3995758bb9635e3814af7ed2449e1
MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/wise/wise-2.2.0.ebuild b/sci-biology/wise/wise-2.2.0.ebuild
deleted file mode 100644
index f738f66ef751..000000000000
--- a/sci-biology/wise/wise-2.2.0.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.2.0.ebuild,v 1.12 2010/10/02 15:08:42 dilfridge Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Intelligent algorithms for DNA searches"
-HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}2/${PN}${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS="~alpha ia64 ~sparc x86 ~amd64"
-
-RDEPEND="~sci-biology/hmmer-2.3.2"
-DEPEND="${RDEPEND}
- app-shells/tcsh
- dev-lang/perl
- virtual/latex-base"
-
-S="${WORKDIR}"/${PN}${PV}
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
- epatch "${FILESDIR}"/${P}-glibc-2.10.patch
- cd "${S}"/src
-# if use threads; then
-# append-flags "-DPTHREAD"
-# sed -e "s/#EXTRALIBS = -lpthread/EXTRALIBS = -lpthread/" -i makefile || die
-# fi
- sed -e "s/CC = cc/CC = $(tc-getCC)/" \
- -e "s/CFLAGS = -c -O/CFLAGS = -c ${CFLAGS}/" \
- -i makefile || die
- cd "${S}"/docs
- cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex
- cat wise2api.tex temp.tex apiend.tex > api.tex
- epatch "${FILESDIR}"/${PN}-api.tex.patch
-}
-
-src_compile() {
- cd src
- make all || die
- cd "${S}"/docs
- for i in api appendix dynamite wise2 wise3arch; do
- latex ${i} || die
- latex ${i} || die
- dvips ${i}.dvi -o || die
- done
-}
-
-src_install() {
- dobin "${S}"/src/bin/* || die "Failed to install program"
- dolib "${S}"/src/base/libwisebase.a || die "Failed to install libwisebase"
- dolib "${S}"/src/dynlibsrc/libdyna.a || die "Failed to install libdyna"
- dobin "${S}"/src/dynlibsrc/testgendb || die "Failed to install testgendb"
- dolib "${S}"/src/models/libmodel.a || die "Failed to install libmodel"
- insinto /usr/share/${PN}
- doins -r "${S}"/wisecfg || die "Failed to install wisecfg"
- insinto /usr/share/doc/${PF}
- doins "${S}"/docs/*.ps || die "Failed to install documentation"
- newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
-}
-
-src_test() {
- cd "${S}"/src
- WISECONFIGDIR="${S}/wisecfg" make test || die
-}